Bird and mammal sex-chromosome orthologs map to the same autosomal region in a salamander (ambystoma)

We tested hypotheses concerning the origin of bird and mammal sex chromosomes by mapping the location of amniote sex-chromosome loci in a salamander amphibian (Ambystoma). We found that ambystomatid orthologs of human X and chicken Z sex chromosomes map to neighboring regions of a common Ambystoma linkage group 2 (ALG2). We show statistically that the proportion of human X and chicken Z orthologs observed on ALG2 is significantly different from the proportion that would be expected by chance. We further show that conserved syntenies between ALG2 and amniote chromosomes are identified as overlapping conserved syntenies when all available chicken (N = 3120) and human (N = 14,922) RefSeq orthologs are reciprocally compared. In particular, the data suggest that chromosomal regions from chicken chromosomes (GGA) Z and 4 and from human chromosomes (HSA) 9, 4, X, 5, and 8 were linked ancestrally. A more distant outgroup comparison with the pufferfish Tetraodon nigroviridis reveals ALG2/GGAZ/HSAX syntenies among three pairs of ancestral chromosome duplicates. Overall, our results suggest that sex chromosomal regions of birds and mammals were recruited from a common ancestral chromosome, and thus our findings conflict with the currently accepted hypothesis of separate autosomal origins. We note that our results were obtained using the most immediate outgroup to the amniote clade (mammals, birds, and other reptiles) while the currently accepted hypothesis is primarily based upon conserved syntenies between in-group taxa (birds and mammals). Our study illustrates the importance of an amphibian outgroup perspective in identifying ancestral amniote gene orders and in reconstructing patterns of vertebrate sex-chromosome evolution.     

AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS

Abstract— Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2—4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.     

The postcranial skeleton of the Devonian tetrapod Tulerpeton curtum Lebedev

Postcranial remains of the Russian Late Devonian tetrapod Tulerpeton include the hexadactylous fore limb, hind limb, anocleithral pectoral girdle, squamation, and associated disarticulated postcranial bones. A cladistic analysis indicates that Tulerpeton is a reptiliomorph stem-group amniote and the earliest known crown-group tetrapod: Acanthostega and Ichthyostega are successively more derived plesion stem-group tetrapods and do not consititute a monophyletic ichthyostegalian radiation. Previous analyses suggesting a profound split in tetrapod phylogeny are thereby corroborated, and likewise the interpretation of Westlothiana as a stem-group amniote. The divergence of reptiliomorphs from batrachomorphs occurred before the Devonian-Carboniferous boundary. Tulerpeton originates from an entirely aquatic environment with a diverse fish fauna. The morphologies of its limbs and those of Devonian stem-tetrapods suggest that dactyly predates the elaboration of the carpus and tarsus, and that Polydactyly persisted after the evolutionary divergence of the principal lineages of living tetrapods. The apparent absence of a branchial lamina and gill skeleton suggests that Tulerpeton was primarily air-breathing, whereas contemporary stem-group tetrapods and more recent batrachomorphs retained greater emphasis on gill-breathing.     

Ecological versus phylogenetic determinants of helminth parasite community richness

Summary We examine patterns of community richness among intestinal parasitic helminth communities in fishes, herptiles, birds and mammals with respect to the comparative number of component species in a host population. We show that terrestrial hosts have, on average, fewer component species than aquatic hosts. We also show that the mean number of component species in aquatic hosts increases from fishes through herptiles to birds before declining slightly in mammals. For terrestrial hosts, the mean number of component species increases from herptiles, through birds, reaching a maximum in mammals. We conclude that: (i) habitat of the host is more important in determining community richness than is host phylogeny; (ii) the phenomenon of host capture may be largely responsible for increased species richness in some host groups; (iii) aquatic birds harbour the richest intestinal helminth communities; and (iv) as we interpret them, our data refute the time hypothesis, which would predict that fishes as the oldest lifestyle should have the richest helminth communities.Order of authorship determined by random draw and does not imply seniority.     

BioEssays 10/2020

Frequent independent origins of environmental sex determination (ESD) are assumed within amniotes. However, the phylogenetic distribution of sex-determining modes suggests that ESD is likely very ancient and may be homologous across ESD groups. Sex chromosomes are demonstrated to be old and stable in endothermic (mammals and birds) and many ectothermic (non-avian reptiles) lineages, but they are mostly non-homologous between individual amniote lineages. The phylogenetic pattern may be explained by ancestral ESD with multiple transitions to later evolutionary stable genotypic sex determination. It is pointed out here that amniote ESD shares several key aspects with sequential hermaphroditism of fishes such as a lack of sex differences in genomes, biased population sex ratios, and potentially also molecular mechanism related to general stress responses. Here, it is speculated that ESD evolves via a heterochronic shift of the sensitive period of sex change from the adult to the embryonic stage in a hermaphroditic amniote ancestor. Also see the video abstract here https://youtu.be/q2mjtlCefu4 .     

The relationship between body mass and relative investment in testes mass in amniotes and other vertebrates

In terrestrial placental mammals, there is a well‐known negative allometric relationship between body mass and relative investment in testes mass. Such a negative relationship means that males of relatively monogamous small species invest proportionately more in their reproductive tissues than males of more polyandrous larger species. The selective pressure responsible for this relationship remains unclear and is it not known if this is a general allometric relationship that is similar across all vertebrate lineages. To investigate this, we conducted the first comparison of relationships between body mass and testes mass (using percentage testes mass as the dependent variable) across a variety of vertebrate groups. In all amniote lineages examined, the allometric relationship between body mass and testes mass was relatively strong and negative. We show, for the first time, that reptiles, birds and terrestrial placental mammals followed the same allometric relationship and, contrary to previous expectations, this relationship is sigmoidal rather than linear. Within this data set, there was no significant difference between this general amniote relationship and any of the 13 orders of reptiles, birds and terrestrial placental mammals examined. As a result, we propose that a sigmoidal relationship should be considered the default assumption for the form of the body mass – testes mass relationship within the amniote lineage. However, we also identify significant differences within some additional mammal groups (marsupials, bats and cetaceans). In each of these cases, only some sub‐groupings differed significantly from the general amniote relationship. In contrast to the amniotes, the relationship is relatively weak and positive in teleost fish and frogs suggesting that a negative allometric relationship is not universal in vertebrates. We explore whether variation in the body mass – testes mass relationships can be linked to sperm competition or a variety of ecological characteristics, either for amniotes in particular or vertebrates in general.     

The first specimen of Archaeopteryx from the Upper Jurassic Mörnsheim Formation of Germany

From an initial isolated position as the oldest evolutionary prototype of a bird, Archaeopteryx has, as a result of recent fossil discoveries, become embedded in a rich phylogenetic context of both more and less crownward stem-group birds. This has prompted debate over whether Archaeopteryx is simply a convergently bird-like non-avialan theropod. Here we show, using the first synchrotron microtomographic examination of the genus, that the eighth or Daiting specimen of Archaeopteryx possesses a character suite that robustly constrains it as a basal avialan (primitive bird). The specimen, which comes from the Mörnsheim Formation and is thus younger than the other specimens from the underlying Solnhofen Formation, is distinctive enough to merit designation as a new species, Archaeopteryx albersdoerferi sp. nov., but is recovered in close phylogenetic proximity to Archaeopteryx lithographica. Skeletal innovations of the Daiting specimen, such as fusion and pneumatization of the cranial bones, well vascularized pectoral girdle and wing elements, and a reinforced configuration of carpals and metacarpals, suggest that it may have had more characters seen in flying birds than the older Archaeopteryx lithographica. These innovations appear to be convergent on those of more crownward avialans, suggesting that Bavarian archaeopterygids independently acquired increasingly bird-like traits over time. Such mosaic evolution and iterative exploration of adaptive space may be typical for major functional transitions like the origin of flight.     

Morphology of the temporal skull region in tetrapods: research history,functional explanations,and a new comprehensive classification scheme

The morphology of the temporal region in the tetrapod skull traditionally has been a widely discussed feature of vertebrate anatomy. The evolution of different temporal openings in Amniota (mammals, birds, and reptiles), Lissamphibia (frogs, salamanders, and caecilians), and several extinct tetrapod groups has sparked debates on the phylogenetic, developmental, and functional background of this region in the tetrapod skull. This led most famously to the erection of different amniote taxa based on the number and position of temporal fenestrae in their skulls. However, most of these taxa are no longer recognised to represent natural groupings and the morphology of the temporal region is not necessarily an adequate trait for use in the reconstruction of amniote phylogenies. Yet, new fossil finds, most notably of parareptiles and stem-turtles, as well as modern embryological and biomechanical studies continue to provide new insights into the morphological diversity of the temporal region. Here, we introduce a novel comprehensive classification scheme for the various temporal morphotypes in all Tetrapoda that is independent of phylogeny and previous terminology and may facilitate morphological comparisons in future studies. We then review the history of research on the temporal region in the tetrapod skull. We document how, from the early 19th century with the first recognition of differences in the temporal region to the first proposals of phylogenetic relationships and their assessment over the centuries, the phylogenetic perspective on the temporal region has developed, and we highlight the controversies that still remain. We also compare the different functional and developmental drivers proposed for the observed morphological diversity and how the effects of internal and external factors on the structure of the tetrapod skull have been interpreted.     

Evolving nonapeptide mechanisms of gregariousness and social diversity in birds

Of the major vertebrate taxa, Class Aves is the most extensively studied in relation to the evolution of social systems and behavior, largely because birds exhibit an incomparable balance of tractability, diversity, and cognitive complexity. In addition, like humans, most bird species are socially monogamous, exhibit biparental care, and conduct most of their social interactions through auditory and visual modalities. These qualities make birds attractive as research subjects, and also make them valuable for comparative studies of neuroendocrine mechanisms. This value has become increasingly apparent as more and more evidence shows that social behavior circuits of the basal forebrain and midbrain are deeply conserved (from an evolutionary perspective), and particularly similar in birds and mammals. Among the strongest similarities are the basic structures and functions of avian and mammalian nonapeptide systems, which include mesotocin (MT) and arginine vasotocin (VT) systems in birds, and the homologous oxytocin (OT) and vasopressin (VP) systems, respectively, in mammals. We here summarize these basic properties, and then describe a research program that has leveraged the social diversity of estrildid finches to gain insights into the nonapeptide mechanisms of grouping, a behavioral dimension that is not experimentally tractable in most other taxa. These studies have used five monogamous, biparental finch species that exhibit group sizes ranging from territorial male-female pairs to large flocks containing hundreds or thousands of birds. The results provide novel insights into the history of nonapeptide functions in amniote vertebrates, and yield remarkable clarity on the nonapeptide biology of dinosaurs and ancient mammals. This article is part of a Special Issue entitled Oxytocin, Vasopressin, and Social Behavior.     

The evolution of body size in birds. II. The role of reproductive power

Given that body mass evolves non-randomly in birds, it is important to ask what factors might be responsible. One suggestion is that the rate at which individuals turn resources into offspring, termed reproductive power, might explain this non-randomness. This is because, in mammals, the body mass with the highest reproductive power is the most common (modal) one. Reproductive power was estimated for birds from data on energetic content of eggs and population productivity. According to the formulation of Brown et al. (1993), reproductive power is composed of two component processes: acquisition (acquiring resources and storing them in reproductive biomass) and conversion (converting reproductive biomass into offspring). As with mammals, estimates of reproductive power indicate that the most common body mass in birds is also the body mass that maximizes reproductive power. The relationship between reproductive power and diversity is different for species smaller than this modal body mass when compared to those that are larger. The relationship of body mass and reproductive power is different between birds and mammals in two ways: (1) the body mass that maximizes reproductive power is smaller in birds (33g) than in mammals (100g), and (2) mammals generate more reproductive power than an equivalent-sized bird. Reproductive power is determined primarily by acquisition in small birds and mammals, while it is determined by conversion in the largest birds and mammals. It is likely that reproductive power is closely tied to the evolution and diversification of body masses because it constrains the ways in which traits affecting fitness can evolve.     

Ovarian steroid synthesis and the hormonal control of the elasmobranch reproductive tract

Synopsis The reproductive biology of the chondricthyan fishes is remarkably sophisticated. Using both oviparous and viviparous reproductive modes, the group has generally adapted the style of bringing forth relatively few young at one time, each representing the investment of a great deal of maternal energy. The oviparous species foreshadow the situation common in oviparous reptiles and universal in birds. On the other hand, viviparous species range from simple internal incubators, in which large yolked eggs are retained, to other species in which the complexity of placentation and yolk reduction approach the eutherian condition. Further, in certain viviparous elasmobranchs the phenomenon of histotrophic nutrition attains an importance and complexity not seen in any other vertebrate group including mammals. Internal fertilization and amniote patterns of reproductive tract development also operate in virtually all elasmobranchs. The summary of work presented here suggests that these female reproductive styles are associated with a reproductive endocrinology which is the archetype for amniote vertebrates.     

Energetics, body size, and the limits to endothermy

The scaling rate of metabolism with respect to body mass is analysed. Scaling of heat production implies that scaling also exists between temperature regulation and body mass. Most vertebrates follow a Kleiber relation down to a "critical mass, below which the scaling of metabolism must be changed to ensure the maintenance of endothermy. Such an adjustment is found interspecifically in birds and mammals, and is found intraspecifically in mammals during post-natal growth. If the Kleiber scaling relation is maintained below the critical mass, mammals and birds shiR from endothermic temperature regulation (above critical mass) to endothermy with obligatory torpor (below critical mass). If the Kleiber relation is followed to masses far below the critical mass, ectothermy results. Critical mass varies inversely with the level of energy expenditure, which therefore accounts for the fact that most mammals and birds are endotherms and most reptiles and fish are ectotherms. The same relationship permits the facultative endothermy found in some insects and plants.
The scaling relations existing among rate of metabolism, endothermy, and body mass can be written as a modification of the Kleiber relation. This analysis suggests that any organism, irrespective of phylogenetic position, can be endothermic at any body size, if its rate of metabolism is high enough, or can be endothermic with any rate of metabolism, if it is large enough. Consequently, it is difficult to distinguish minimal endothermy from inertial homoiothermy in animals having a large mass. The boundary conditions for effective endothermy are similar to the relationship described between metabolism and mass in the evolution of endothermy through a decrease in mass in the phylogeny of mammals. Even though endothermy may evolve with an increase in mass, its perfection may always require an evolutionary decrease in mass.     

Social Mating System and Sex-Biased Dispersal in Mammals and Birds: A Phylogenetic Analysis

The hypothesis that patterns of sex-biased dispersal are related to social mating system in mammals and birds has gained widespread acceptance over the past 30 years. However, two major complications have obscured the relationship between these two behaviors: 1) dispersal frequency and dispersal distance, which measure different aspects of the dispersal process, have often been confounded, and 2) the relationship between mating system and sex-biased dispersal in these vertebrate groups has not been examined using modern phylogenetic comparative methods. Here, we present a phylogenetic analysis of the relationship between mating system and sex-biased dispersal in mammals and birds. Results indicate that the evolution of female-biased dispersal in mammals may be more likely on monogamous branches of the phylogeny, and that females may disperse farther than males in socially monogamous mammalian species. However, we found no support for a relationship between social mating system and sex-biased dispersal in birds when the effects of phylogeny are taken into consideration. We caution that although there are larger-scale behavioral differences in mating system and sex-biased dispersal between mammals and birds, mating system and sex-biased dispersal are far from perfectly associated within these taxa.     

Early Mesozoic Coexistence of Amniotes and Hepadnaviridae

Hepadnaviridae are double-stranded DNA viruses that infect some species of birds and mammals. This includes humans, where hepatitis B viruses (HBVs) are prevalent pathogens in considerable parts of the global population. Recently, endogenized sequences of HBVs (eHBVs) have been discovered in bird genomes where they constitute direct evidence for the coexistence of these viruses and their hosts from the late Mesozoic until present. Nevertheless, virtually nothing is known about the ancient host range of this virus family in other animals. Here we report the first eHBVs from crocodilian, snake, and turtle genomes, including a turtle eHBV that endogenized >207 million years ago. This genomic “fossil” is >125 million years older than the oldest avian eHBV and provides the first direct evidence that Hepadnaviridae already existed during the Early Mesozoic. This implies that the Mesozoic fossil record of HBV infection spans three of the five major groups of land vertebrates, namely birds, crocodilians, and turtles. We show that the deep phylogenetic relationships of HBVs are largely congruent with the deep phylogeny of their amniote hosts, which suggests an ancient amniote–HBV coexistence and codivergence, at least since the Early Mesozoic. Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene. We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs. Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts.     

Evolutionary loss of ascorbic acid synthesizing ability

The ability to synthesize ascorbic acid has been found only in terrestrial vertebrates. The ability is not present in certain passerine birds, in fruit-eating bats, in guinea-pigs and in Anthropoidea. We postulate that these species lost this ability by a neutral evolutionary change that occurred sporadically by mutation. The change was adopted in the genetic make-up of a few groups of birds and mammals that are widely-scattered in phylogeny. Many herbivorous vertebrate species which consume diets high in ascorbic acid have retained the ability to synthesize it, so that its loss does not appear to be adaptive.     

A review of the lower actinopterygian phylogeny

A review of lower actinopterygian phylogeny has led us to the conclusion that the Cladistia are the sister group of Recent actinopterygians (Actinopteri) and that the extinct Palaeonisciformes are a paraphyletic group, comprising stem-group actinopterygians (e.g. Cheirolepis ), stem-group actinopterans (e.g. Moythomasia ) and relatives of higher actinopterans such as Pteronisculus . Our analysis further concluded that the Acipenseriformes formed a clade together with Saurichthys and Birgeria , which was most parsimoniously resolved when the Acipenseriformes and Saurichthys were sister groups.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 511−525.     

Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships [published erratum appears in Mol Biol Evol 1991 May;8(3):398]

The 18S ribosomal RNAs of 21 tetrapods were sequenced and aligned with five published tetrapod sequences. When the coelacanth was used as an outgroup, Lissamphibia (living amphibians) and Amniota (amniotes) were found to be statistically significant monophyletic groups. Although little resolution was obtained among the lissamphibian taxa, the amniote sequences support a sister-group relationship between birds and mammals. Portions of the 28S ribosomal RNA (rRNA) molecule in 11 tetrapods also were sequenced, although the phylogenetic results were inconclusive. In contrast to previous studies, deletion or down- weighting of base-paired sites were found to have little effect on phylogenetic relationships. Molecular evidence for amniote relationships is reviewed, showing that three genes (beta-hemoglobin, myoglobin, and 18S rRNA) unambiguously support a bird-mammal relationship, compared with one gene (histone H2B) that favors a bird- crocodilian clade. Separate analyses of four other genes (alpha- crystallin A, alpha-hemoglobin, insulin, and 28S rRNA) and a combined analysis of all sequence data are inconclusive, in that different groups are defined in different analyses and none are strongly supported. It is suggested that until sequences become available from a broader array of taxa, the molecular evidence is best evaluated at the level of individual genes, with emphasis placed on those studies with the greatest number of taxa and sites. When this is done, a bird-mammal relationship is most strongly supported. When regarded in combination with the morphological evidence for this association, it must be considered at least as plausible as a bird-crocodilian relationship.      

Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins

The phylogenetic relationships of eukaryotic aspartic proteinases were reconstructed in order to understand the origin of pregnancy-associated glycoproteins (PAGs), which constitute a large gene family expressed in the trophoblast and placenta of mammals in the order Artiodactyla. The phylogeny supported the hypothesis that PAGs originated in mammals, being most closely related to a group of PAG-like molecules (including rodent pepsin F) found in other mammalian orders. These two groups in turn form a sister group to a group of digestive enzymes from birds and mammals, which includes pepsin A. Sequence similarity in the promoter region of artiodactyl PAGs and mouse pepsin F also supported a close relationship between these genes. Ancestral sequence reconstruction revealed that, at the residues corresponding to positions 148-150 of pepsin A, in the ancestor of artiodactyl PAGs the motif QNL was replaced by EPV; and EPV (or occasionally EPI) is conserved at these sites in known PAGs. The conservation of this ancestral change suggests that it may be important to PAG function, particularly the fact that PAGs lack proteinase activity in spite of the conservation of active site residues in most PAGs.     

Phylogenetic reconstruction of parental-care systems in the ancestors of birds

Due to the controversy surrounding incipient avian parental care, ancestral parental care systems were reconstructed in a phylogeny including major extant amniote lineages. Using two different resolutions for the basal avian branches, transitions between the states no care, female care, biparental care and male care were inferred for the most basal branches of the tree. Uniparental female care was inferred for the lineage to birds and crocodiles. Using a phylogeny where ratites and tinamous branch off early and an ordered character-state assumption, a transition to biparental care was inferred for the ancestor of birds. This ancestor could be any organism along the lineage leading from the crocodile-bird split up to modern birds, not necessarily the original bird. We discuss the support for alternative avian phylogenies and the homology in parental care between crocodiles and birds. We suggest that the phylogenetic pattern should be used as a starting point for a more detailed analysis of parental care systems in birds and their relatives.